Sooty mangabeys are African Old World primates that are naturally infected with SIV, have high plasma SIV levels and yet do not progress to AIDS To understand the immune basis of this protected state, SIV-specific CTL activity was studied in sooty mangabeys with natural SIV infection and following experimental infection with SIVmac239 SIV-specific CTL activity was analysed in 12 naturally infected sooty mangabeys SIV-specific CTL were not detectable in fresh PBMC from 7 of 7 animals, even when tested at high effector to target ratios, suggesting the absence of circulating activated SIV-specific CTL Following ex vivo antigen-specific stimulation, the response was heterogeneous Vigorous SIV-specific CTL activity was detectable in only 4/12 animals It remained undetectable or inconsistently present in 5/12 animals and detectable at low levels in 3/12 animals No correlation was observed between the magnitude of viral load and the strength of SIV-specific CTL activity SIV-specific CTL clones were isolated from SIVmac239 and naturally infected sooty mangabeys Clones with activity against gag, env and nef proteins mapped to highly conserved regions of the SIV genome An env-specific epitope maps to a highly conserved 9-mer peptide, YVPCHIRQI, located just beyond the V4 region of gp120, while a gag epitope was localized to a 12-mer peptide in p27 (aa 281-292) These epitopes are immunodominant, as bulk CTL lysed targets presenting the epitope to an extent comparable to targets expressing the entire protein A single nef-specific CTL clone was isolated from a naturally infected sooty mangabey and the 20-mer epitope maps to aa 21-40 Follow up of these animals may shed light on the interactions between virus and CTL that result in apathogenic SIV infection